NAME

       Bio::SeqEvolution::DNAPoint - evolve a sequence by point mutations

SYNOPSIS

         # $seq is a Bio::PrimarySeqI to mutate
         $evolve = Bio::SeqEvolution::Factory->new (-rate => 5,
                                                    -seq => $seq,
                                                    -identity => 50
                                                    );
         $newseq = $evolve->next_seq;

DESCRIPTION

       Bio::SeqEvolution::DNAPoint implements the simplest evolution model: nucleotides change by
       point mutations, only. Transition/transversion rate of the change, rate(), can be set.

       The new sequences are named with the id of the reference sequence added with a running
       number. Placing a new sequence into a factory to be evolved resets that counter. It can
       also be called directly with reset_sequence_counter.

       The default sequence type returned is Bio::PrimarySeq. This can be changed to any
       Bio::PrimarySeqI compliant sequence class.

       Internally the probability of the change of one nucleotide is mapped to scale from 0 to
       100. The probability of the transition occupies range from 0 to some value. The remaining
       range is divided equally among the two transversion nucleotides. A random number is then
       generated to pick up one change.

       Not that the default transition/transversion rate, 1:1, leads to observed
       transition/transversion ratio of 1:2 simply because there is only one transition
       nucleotide versus two transversion nucleotides.

FEEDBACK

   Mailing Lists
       User feedback is an integral part of the evolution of this and other Bioperl modules. Send
       your comments and suggestions preferably to the Bioperl mailing list.  Your participation
       is much appreciated.

         bioperl-l@bioperl.org                  - General discussion
         http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

   Support
       Please direct usage questions or support issues to the mailing list:

       bioperl-l@bioperl.org

       rather than to the module maintainer directly. Many experienced and reponsive experts will
       be able look at the problem and quickly address it. Please include a thorough description
       of the problem with code and data examples if at all possible.

   Reporting Bugs
       Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their
       resolution. Bug reports can be submitted via the web:

         https://github.com/bioperl/bioperl-live/issues

AUTHOR

         Heikki Lehvaslaiho E<lt>heikki at bioperl dot orgE<gt>

CONTRIBUTORS

       Additional contributor's names and emails here

APPENDIX

       The rest of the documentation details each of the object methods.  Internal methods are
       usually preceded with a _

   seq
        Title   : seq
        Usage   : $obj->seq($newval)
        Function: Set the sequence object for the original sequence
        Returns : The sequence object
        Args    : newvalue (optional)

       Setting this will reset mutation and generated mutation counters.

   set_mutated_seq
         Title   : seq_mutated_seq
         Usage   : $obj->set_mutated_seq($newval)
         Function: In case of mutating a sequence with multiple evolvers, this
         Returns : set_mutated_seq
         Args    : newvalue (optional)

   rate
         Title   : rate
         Usage   : $obj->rate($newval)
         Function: Set the transition/transversion rate.
         Returns : value of rate
         Args    : newvalue (optional)

       Transition/transversion ratio is an observed attribute of an sequence comparison. We are
       dealing here with the transition/transversion rate that we set for our model of sequence
       evolution.

       Note that we are using standard nucleotide alphabet and that there can there is only one
       transition versus two possible transversions. Rate 2 is needed to have an observed
       transition/transversion ratio of 1.

   next_seq
         Title   : next_seq
         Usage   : $obj->next_seq
         Function: Evolve the reference sequence to desired level
         Returns : A new sequence object mutated from the reference sequence
         Args    : -

   mutate
         Title   : mutate
         Usage   : $obj->mutate
         Function: mutate the sequence at the given location according to the model
         Returns : true
         Args    : integer, start location of the mutation, required argument

       Called from next_seq().